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Update README.md
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meenachakra authored Mar 7, 2023
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Expand Up @@ -143,7 +143,7 @@ This section contains a description of the additional parameters in the config f
* *Terminology note* - minimizers are very similar to kmers; for a more detailed description of what they are, please see [the Kraken2 paper](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1891-0).
* `minimizer_thresh_viral` (default `0`). This parameter can take any value >= 0 and specifies an additional requirement for a viral species to be considered true positive in a sample. E.g., if this parameter is 10, that means at least one genome of the species must have 10+ of its unique minimizers covered by sample reads.
* `cov_thresh_bacterial` and `minimizer_thresh_bacterial` are the analogous parameters for filtering bacterial species.
* Sample sequencing depth may affect the choice of bacterial/viral coverage thresholds - please see our suggested coverage thresholds by sequencing depth, below. These suggestions were based on evaluating the sensitivity/specificity (TPR/FDR) tradeoff at various coverage thresholds and sequencing depths, as described in our manuscript in greater detail. ![suggested coverage thresholds by sequencing depth](https://github.com/bhattlab/phanta/blob/main/Suggested%20Coverage%20Thresholds%20by%20Seq%20Depth.png).
* Sample sequencing depth may affect the choice of bacterial/viral coverage thresholds - please see our suggested coverage thresholds by sequencing depth, below. These suggestions were based on evaluating the sensitivity/specificity (TPR/FDR) tradeoff at various coverage thresholds and sequencing depths, as described in our manuscript in greater detail. ![suggested coverage thresholds by sequencing depth](https://github.com/bhattlab/phanta/blob/main/Suggested%20Coverage%20Thresholds%20by%20Seq%20Depth.png)
* As of release 1.1, upon user request we have also added coverage and minimizer parameters for archaeal and eukaryotic species (`cov_thresh_arc`, `cov_thresh_euk`, `minimizer_thresh_arc`, `minimizer_thresh_euk`).

### Parameters under *Specifications for step three - per-species abundance estimation*
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